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<h1>
<a href="index.html">AQUA</a></h1>

<address>
Jurgen Doreleijers, Madison, <a href="mailto:jurgenfd@gmail.com">jurgenfd@gmail.com</a></address>

<address>
Ton Rullmann, Utrecht</address>

<br>&nbsp;</td>

<td>
<blockquote>
<div align=right><img SRC="aqua.gif" height=108 width=108 align=RIGHT></div>
</blockquote>
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<h2>

<hr WIDTH="100%"></h2>

<h2>
HOW_TO_INSTALL</h2>

<h2>
Contents</h2>

<ol>
<li>
<a href="#1. File organization">FILE ORGANIZATION</a></li>

<li>
<a href="#2. Installation (Unix only)">INSTALLATION (Unix only)</a></li>

<li>
<a href="#3. THE FINISHING TOUCH">FINISHING TOUCH</a></li>
</ol>

<h2>

<hr WIDTH="100%"><a NAME="1. File organization"></a>1. File organization</h2>
The top directory contains the following files:
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<ul>
<li>
HISTORY</li>

<li>
<a href="HOW_TO_INSTALL.html">HOW_TO_INSTALL</a></li>

<li>
<a href="HOW_TO_USE.html">HOW_TO_USE</a>&nbsp;</li>

<li>
<a href="NEW.html">NEW</a>&nbsp;&nbsp;</li>

<li>
<b><a href="README.html">README</a></b>&nbsp;</li>

<li>
aqsetup&nbsp;</li>

<li>
aqsetupi&nbsp;</li>
</ul>
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<ul>
<li>
version history</li>

<li>
installation hints (this document)</li>

<li>
instructions for users</li>

<li>
list of new features and changes</li>

<li>
general introduction (recommended to read first)</li>

<li>
script for defining aliases and variables</li>

<li>
idem; intended for interactive use</li>
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<p>and the following subdirectories:
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<li>
bin</li>

<li>
cgi</li>

<li>
data&nbsp;</li>

<li>
doc&nbsp;</li>

<li>
exmpls&nbsp;</li>

<li>
extras</li>

<li>
html</li>

<li>
scripts</li>

<li>
server</li>

<li>
src&nbsp;</li>

<li>
sub&nbsp;</li>
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<ul>
<li>
executables (to be made by 'make'; see below)</li>

<li>
cgi server software (please ignore)</li>

<li>
name-library files</li>

<li>
documentation</li>

<li>
example jobs and output (used by 'make test')</li>

<li>
some useful non-Aqua tools</li>

<li>
html server documentation and examples (please ignore)</li>

<li>
conversion and analysis scripts</li>

<li>
server forms (please ignore)</li>

<li>
main source code files and makefile</li>

<li>
auxiliary source code</li>
</ul>
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<hr WIDTH="100%">
<h2>
<a NAME="2. Installation (Unix only)"></a>2. Installation (Unix only)</h2>
1. Uncompress and unpack the archive (replacing X.Y by the version number
that you down loaded):
<pre>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; tar -xvzf aquaX.Y.tar.Z # or leave out the uncompressing if already done:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; tar -xvf&nbsp; aquaX.Y.tar</pre>

<blockquote>This will create a subdirectory called 'aquaX.Y' in the present
working directory. This subdirectory will be referred to as the aquaroot
throughout this text. The organization of the aquaroot directory is described
above, and should not be changed.</blockquote>

<p><br>2. Go to the 'src' subdirectory and modify the file 'makefile':
<ul>
<li>
insert the proper location of the root directory in the definition of MYROOT
(near the top of the file).</li>

<li>
change the definitions for the compiler (CC) and the optimization flag
(CFLAGS) if necessary. On some systems the gcc compiler may give better
results than cc.</li>
</ul>
3. Build the executables: (There's an auxiliary Fortran program 'exth.f'
which is not really needed. If you cannot compile that file, follow the
instructions in the makefile).
<pre>&nbsp;&nbsp;&nbsp; make</pre>

<blockquote>The installation/compilation may be done by root or by any
user having write permission for the aquaroot directory tree. There is
no "make install". All binaries and data files reside in the aquaroot directory
tree. You may move the tree to a different location afterwards without
recompiling. Just make sure to keep the subdirectory structure intact.</blockquote>

<p><br>4. Localization:
<ul>
<li>
Adapt 'aqsetup' in the top directory:</li>

<ul>
<li>
modify the definitions of AQUAHELPLIST, AQUAHELPPRINT and AQUAHELPURL if
necessary or desired.</li>
</ul>

<li>
In the first line of 'scripts/aquanal.pl' change the path to perl, if necessary.
You need Perl 5 to use this script, see the file 'doc/perl.txt'.</li>
</ul>
5. Test the installation, and cleanup (first go to the 'src' subdirectory):
<pre>&nbsp;&nbsp;&nbsp; make test&nbsp; #optional: test whether installation was succesfull</pre>

<blockquote>If the test fails on a gawk script with messages about "unknown
option -v" or "undefined function toupper", you have to install gawk, the
GNU version of nawk. See the file 'doc/gawk.txt'.
Update: nawk dependency is removed.</blockquote>

<blockquote>If all is well, you might retrieve some disk space by issuing:</blockquote>

<pre>&nbsp;&nbsp;&nbsp; make strip # optional: reduce size of executables by removing symbols
&nbsp;&nbsp;&nbsp; make clean # optional: remove object files</pre>
6. Define the environment variable 'aquaroot' to point to the Aqua top
directory, and initialize:
<pre>&nbsp;&nbsp;&nbsp; cd ..&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # assume we are now back in the Aqua top directory
&nbsp;&nbsp;&nbsp; setenv aquaroot $cwd
&nbsp;&nbsp;&nbsp; source $aquaroot/aqsetupi</pre>

<blockquote>Now you are ready to use Aqua! See the file 'HOW_TO_USE' for
more details.</blockquote>

<hr WIDTH="100%">
<h2>
<a NAME="3. THE FINISHING TOUCH"></a>3. Finishing touch</h2>
1. You may want to store the 'aquaroot' definition in a system-wide definition
file, such as '/etc/cshrc'. An alias for initializing the Aqua setup may
also be defined there (again replacing X.Y by the current version number):
<pre>&nbsp;&nbsp;&nbsp; setenv aquaroot $YOUR_LOCATION/aquaX.Y
&nbsp;&nbsp;&nbsp; alias aqua 'source $aquaroot/aqsetupi'</pre>

<blockquote>I advise you not to import definitions from the 'aqsetup' script
into places like '/etc/cshrc' or '.cshrc'.</blockquote>
2. Procheck upgrade: for Aqua version 1.0 and above to work correctly in
conjunction with Procheck-NMR you have to upgrade to Procheck version 3.4
or higher.
<p>
<hr>
<p>Contact the <a href="mailto:jurgenfd@gmail.com">author</a> 
for help, when required.
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